Contacts of the helix formed by residues 355 - 361 (chain J) in PDB entry 3FKS
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 355 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175J THR* 4.0 5.2 - - - +
353J PHE* 3.3 27.8 + - + -
354J LEU* 1.3 75.2 - - - +
356J ALA* 1.3 62.9 + - - +
357J GLU* 3.4 12.2 - - + +
358J LEU* 3.3 33.1 - - + +
359J PHE* 3.7 2.9 + - - +
366J ALA* 3.5 24.4 + - - +
368J ASN* 2.8 32.6 + - + -
371J LEU* 5.0 1.2 - - - +
400J ARG* 5.2 2.6 + - - -
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Residues in contact with ALA 356 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172J ASP* 4.8 15.7 + - + +
173J ARG 5.7 0.4 - - - +
175J THR* 3.9 18.9 - - + +
354J LEU 3.9 0.6 + - - -
355J GLU* 1.3 72.4 - - - +
357J GLU* 1.3 68.6 + - + +
358J LEU 3.2 0.2 - - - -
359J PHE* 3.2 10.6 + - - +
360J TYR* 3.0 37.1 + - + -
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Residues in contact with GLU 357 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355J GLU* 4.6 13.7 - - + +
356J ALA* 1.3 79.5 - - + +
358J LEU* 1.3 64.9 + - + +
360J TYR 3.7 0.5 + - - -
361J LYS* 3.3 30.9 + - - +
379M GLN* 2.7 40.7 + - - +
382M LYS* 4.5 11.3 + - - -
383M SER* 4.0 8.3 + - - -
8P MET* 6.1 1.2 - - - +
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Residues in contact with LEU 358 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355J GLU* 3.3 32.9 + - + +
356J ALA 3.2 1.0 - - - -
357J GLU* 1.3 77.2 - - + +
359J PHE* 1.3 61.0 + - - +
361J LYS* 3.6 20.3 + - - +
362J GLY 3.6 2.6 + - - -
363J ILE* 3.0 47.5 + - + +
366J ALA* 3.6 17.0 - - + -
367J ILE 3.6 13.2 - - - +
368J ASN* 3.5 36.1 - - + +
400J ARG* 4.8 15.0 - - - +
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Residues in contact with PHE 359 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174J GLN 4.9 5.2 - - - -
175J THR* 3.8 28.7 - - - +
176J GLY* 5.2 2.7 - - - -
355J GLU 3.7 10.3 + - - +
356J ALA* 3.2 12.2 + - - +
358J LEU* 1.3 79.6 - - - +
360J TYR* 1.3 66.2 - + + +
362J GLY* 3.1 16.5 + - - -
363J ILE 3.8 4.5 - - - -
364J ARG* 3.3 71.1 + - + -
365J PRO* 6.1 0.9 - - + -
366J ALA* 3.7 8.0 - - + +
354M LYS* 3.4 37.7 - - - -
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Residues in contact with TYR 360 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174J GLN* 5.3 4.0 + - - +
356J ALA* 3.0 41.9 + - + +
359J PHE* 1.3 83.2 - + + +
361J LYS* 1.3 56.9 + - - +
362J GLY 3.1 1.1 - - - -
364J ARG* 4.8 4.1 + - - +
351M LEU* 3.5 47.4 + - + -
352M ASP* 4.0 9.0 + - - -
353M SER 5.4 1.3 - - - -
354M LYS* 3.2 39.6 + - + +
375M GLN* 3.6 30.8 - - + +
376M GLU* 3.1 33.0 + - - +
379M GLN* 3.8 25.1 - - + +
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Residues in contact with LYS 361 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357J GLU* 3.3 23.4 + - - +
358J LEU* 3.9 21.2 - - - +
359J PHE 3.2 0.8 - - - -
360J TYR* 1.3 77.7 - - - +
362J GLY* 1.3 56.2 + - - +
363J ILE* 3.6 22.7 + - + +
431J LYS* 4.9 2.6 + - - -
376M GLU* 3.7 19.3 - - + +
379M GLN* 4.3 16.8 - - + +
380M THR* 5.2 10.5 - - - +
383M SER* 5.3 6.5 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il